Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userLocal block-wise self attention for normal organ segmentation
78
0
0.0
(
0
)
Added by
Jue Jiang Dr.
Publication date
2019
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
We developed a new and computationally simple local block-wise self attention based normal structures segmentation approach applied to head and neck computed tomography (CT) images. Our method uses the insight that normal organs exhibit regularity in their spatial location and inter-relation within images, which can be leveraged to simplify the computations required to aggregate feature information. We accomplish this by using local self attention blocks that pass information between each other to derive the attention map. We show that adding additional attention layers increases the contextual field and captures focused attention from relevant structures. We developed our approach using U-net and compared it against multiple state-of-the-art self attention methods. All models were trained on 48 internal headneck CT scans and tested on 48 CT scans from the external public domain database of computational anatomy dataset. Our method achieved the highest Dice similarity coefficient segmentation accuracy of 0.85$pm$0.04, 0.86$pm$0.04 for left and right parotid glands, 0.79$pm$0.07 and 0.77$pm$0.05 for left and right submandibular glands, 0.93$pm$0.01 for mandible and 0.88$pm$0.02 for the brain stem with the lowest increase of 66.7% computing time per image and 0.15% increase in model parameters compared with standard U-net. The best state-of-the-art method called point-wise spatial attention, achieved textcolor{black}{comparable accuracy but with 516.7% increase in computing time and 8.14% increase in parameters compared with standard U-net.} Finally, we performed ablation tests and studied the impact of attention block size, overlap of the attention blocks, additional attention layers, and attention block placement on segmentation performance.
rate research
Read More
Although deep convolutional networks have been widely studied for head and neck (HN) organs at risk (OAR) segmentation, their use for routine clinical treatment planning is limited by a lack of robustness to imaging artifacts, low soft tissue contrast on CT, and the presence of abnormal anatomy. In order to address these challenges, we developed a computationally efficient nested block self-attention (NBSA) method that can be combined with any convolutional network. Our method achieves computational efficiency by performing non-local calculations within memory blocks of fixed spatial extent. Contextual dependencies are captured by passing information in a raster scan order between blocks, as well as through a second attention layer that causes bi-directional attention flow. We implemented our approach on three different networks to demonstrate feasibility. Following training using 200 cases, we performed comprehensive evaluations using conventional and clinical metrics on a separate set of 172 test scans sourced from external and internal institution datasets without any exclusion criteria. NBSA required a similar number of computations (15.7 gflops) as the most efficient criss-cross attention (CCA) method and generated significantly more accurate segmentations for brain stem (Dice of 0.89 vs. 0.86) and parotid glands (0.86 vs. 0.84) than CCA. NBSAs segmentations were less variable than multiple 3D methods, including for small organs with low soft-tissue contrast such as the submandibular glands (surface Dice of 0.90).
Accurate and robust segmentation of abdominal organs on CT is essential for many clinical applications such as computer-aided diagnosis and computer-aided surgery. But this task is challenging due to the weak boundaries of organs, the complexity of the background, and the variable sizes of different organs. To address these challenges, we introduce a novel framework for multi-organ segmentation by using organ-attention networks with reverse connections (OAN-RCs) which are applied to 2D views, of the 3D CT volume, and output estimates which are combined by statistical fusion exploiting structural similarity. OAN is a two-stage deep convolutional network, where deep network features from the first stage are combined with the original image, in a second stage, to reduce the complex background and enhance the discriminative information for the target organs. RCs are added to the first stage to give the lower layers semantic information thereby enabling them to adapt to the sizes of different organs. Our networks are trained on 2D views enabling us to use holistic information and allowing efficient computation. To compensate for the limited cross-sectional information of the original 3D volumetric CT, multi-sectional images are reconstructed from the three different 2D view directions. Then we combine the segmentation results from the different views using statistical fusion, with a novel term relating the structural similarity of the 2D views to the original 3D structure. To train the network and evaluate results, 13 structures were manually annotated by four human raters and confirmed by a senior expert on 236 normal cases. We tested our algorithm and computed Dice-Sorensen similarity coefficients and surface distances for evaluating our estimates of the 13 structures. Our experiments show that the proposed approach outperforms 2D- and 3D-patch based state-of-the-art methods.
In this paper, we present a so-called interlaced sparse self-attention approach to improve the efficiency of the emph{self-attention} mechanism for semantic segmentation. The main idea is that we factorize the dense affinity matrix as the product of two sparse affinity matrices. There are two successive attention modules each estimating a sparse affinity matrix. The first attention module is used to estimate the affinities within a subset of positions that have long spatial interval distances and the second attention module is used to estimate the affinities within a subset of positions that have short spatial interval distances. These two attention modules are designed so that each position is able to receive the information from all the other positions. In contrast to the original self-attention module, our approach decreases the computation and memory complexity substantially especially when processing high-resolution feature maps. We empirically verify the effectiveness of our approach on six challenging semantic segmentation benchmarks.
The anchor-based detectors handle the problem of scale variation by building the feature pyramid and directly setting different scales of anchors on each cell in different layers. However, it is difficult for box-wise anchors to guide the adaptive learning of scale-specific features in each layer because there is no one-to-one correspondence between box-wise anchors and pixel-level features. In order to alleviate the problem, in this paper, we propose a scale-customized weak segmentation (SCWS) block at the pixel level for scale customized object feature learning in each layer. By integrating the SCWS blocks into the single-shot detector, a scale-aware object detector (SCOD) is constructed to detect objects of different sizes naturally and accurately. Furthermore, the standard location loss neglects the fact that the hard and easy samples may be seriously imbalanced. A forthcoming problem is that it is unable to get more accurate bounding boxes due to the imbalance. To address this problem, an adaptive IoU (AIoU) loss via a simple yet effective squeeze operation is specified in our SCOD. Extensive experiments on PASCAL VOC and MS COCO demonstrate the superiority of our SCOD.
Existing video polyp segmentation (VPS) models typically employ convolutional neural networks (CNNs) to extract features. However, due to their limited receptive fields, CNNs can not fully exploit the global temporal and spatial information in successive video frames, resulting in false-positive segmentation results. In this paper, we propose the novel PNS-Net (Progressively Normalized Self-attention Network), which can efficiently learn representations from polyp videos with real-time speed (~140fps) on a single RTX 2080 GPU and no post-processing. Our PNS-Net is based solely on a basic normalized self-attention block, equipping with recurrence and CNNs entirely. Experiments on challenging VPS datasets demonstrate that the proposed PNS-Net achieves state-of-the-art performance. We also conduct extensive experiments to study the effectiveness of the channel split, soft-attention, and progressive learning strategy. We find that our PNS-Net works well under different settings, making it a promising solution to the VPS task.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
